Merge pull request #65 from joshwlambert/richel

Use correct X axis

R/plot_daisie_data.R

@@ -17,10 +17,11 @@ plot_daisie_data <- function(daisie_data) {
   t <- DAISIEmainland::daisie_data_to_tables(daisie_data)
 
   p <- ggplot2::ggplot(t$colonists_general) +
-    ggplot2::scale_x_continuous(
-      name = "Time",
-      limits = c(0, t$header$island_age)
-    ) + ggplot2::theme(
+    ggplot2::scale_x_reverse(
+      name = "Time before present",
+      limits = c(t$header$island_age, 0)
+    ) +
+    ggplot2::theme(
       axis.title.y = ggplot2::element_blank(),
       axis.text.y = ggplot2::element_blank(),
       axis.ticks.y = ggplot2::element_blank()
@@ -126,7 +127,7 @@ plot_daisie_data <- function(daisie_data) {
     ggplot2::aes(
       x = branching_times,
       y = y,
-      xend = t$header$island_age,
+      xend = 0,
       yend = y,
       color = stac_str
     )

tests/testthat/test-plot_daisie_mainland_data.R

@@ -78,3 +78,33 @@ test_that("many clades", {
   )
   plot_daisie_mainland_data(daisie_mainland_data, replicate_index = 1)
 })
+
+test_that("Issue 64: use time before present", {
+
+  # The Endemic_singleton_MaxAge island species are plotted near
+  # the edge of the plot but they should have the longest line.
+  # This makes me think that the plot_daisie_mainland_data function
+  # should plot "Time before present" on the x-axis.
+  set.seed(
+    1,
+    kind = "Mersenne-Twister",
+    normal.kind = "Inversion",
+    sample.kind = "Rejection"
+  )
+
+  daisie_mainland_data <- DAISIEmainland::sim_island_with_mainland(
+    total_time = 1,
+    m = 100,
+    island_pars = c(1.0, 0.5, 10, 0.1, 0.5),
+    mainland_ex = 2,
+    mainland_sample_prob = 1,
+    mainland_sample_type = "complete",
+    replicates = 1,
+    verbose = FALSE
+  )
+
+  DAISIEmainland::plot_daisie_mainland_data(
+    daisie_mainland_data = daisie_mainland_data,
+    replicate_index = 1
+  )
+})